SMTL ID : 7rqx.1

Cryo-EM structure of the full-length TRPV1 with RTx at 25 degrees Celsius, in an intermediate-open state, class A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-tetramer

Ligands

8 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.1: 19 residues within 4Å: Chain A: F.436, N.437, V.440, Y.441, L.443, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555, D.707 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.443 Salt bridges: A:E.513 pi-Cation interactions: A:F.516 LBN.5: 16 residues within 4Å: Chain A: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, V.457, G.470, F.473, R.474, T.476, G.477, L.480 Chain C: N.628 Ligands: 6OU.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.446, A:I.447, A:A.450, A:Y.454, A:F.473, A:F.473, A:F.473, A:R.474 LBN.9: 19 residues within 4Å: Chain B: F.436, N.437, V.440, Y.441, L.443, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555, D.707 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.443 Salt bridges: B:E.513 pi-Cation interactions: B:F.516 LBN.14: 16 residues within 4Å: Chain B: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, V.457, G.470, F.473, R.474, T.476, G.477, L.480 Chain D: N.628 Ligands: 6OU.24 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:I.446, B:I.447, B:A.450, B:Y.454, B:F.473, B:F.473, B:F.473, B:F.473, B:R.474 LBN.16: 16 residues within 4Å: Chain B: N.628 Chain C: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, V.457, G.470, F.473, R.474, T.476, G.477, L.480 Ligands: 6OU.10 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.446, C:I.447, C:A.450, C:Y.454, C:F.473, C:F.473, C:F.473, C:F.473, C:R.474 LBN.17: 19 residues within 4Å: Chain C: F.436, N.437, V.440, Y.441, L.443, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555, D.707 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.443 Salt bridges: C:E.513 pi-Cation interactions: C:F.516 LBN.21: 17 residues within 4Å: Chain A: N.628 Chain D: L.443, I.446, I.447, A.450, A.451, Y.453, Y.454, R.455, V.457, G.470, F.473, R.474, T.476, G.477, L.480 Ligands: 6OU.20 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.446, D:I.447, D:A.450, D:Y.454, D:F.473, D:F.473, D:F.473, D:R.474 LBN.23: 19 residues within 4Å: Chain D: F.436, N.437, V.440, Y.441, L.443, Y.444, I.447, L.480, S.483, G.484, Y.487, F.488, R.491, S.512, E.513, F.516, Y.554, Y.555, D.707 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.443 Salt bridges: D:E.513 pi-Cation interactions: D:F.516

12 x 6OU: [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate(Non-covalent)

6OU.2: 15 residues within 4Å: Chain A: F.448, A.451, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.448, A:I.479, A:V.527, A:Y.530, A:Y.530 6OU.4: 13 residues within 4Å: Chain A: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain C: L.585, V.586, F.589, T.593, L.630 Ligands: LBN.5, 6OU.13 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:I.446, A:W.549, A:W.549, C:F.589, C:F.589, C:F.589, C:F.589 Hydrogen bonds: A:Y.454 6OU.6: 18 residues within 4Å: Chain A: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain D: Y.584, L.585, L.588, S.629, L.630, Y.631, C.634, L.635, F.638 Ligands: 6OU.24, 6EU.26 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:I.660, A:I.661, A:L.664, D:Y.631, D:F.638 Salt bridges: A:K.656, A:K.656 Hydrogen bonds: D:S.629 6OU.10: 13 residues within 4Å: Chain B: L.585, V.586, F.589, T.593, L.630 Chain C: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: LBN.16, 6OU.22 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:I.446, C:W.549, C:W.549, B:F.589, B:F.589, B:F.589, B:F.589 Hydrogen bonds: C:Y.454 6OU.11: 15 residues within 4Å: Chain B: F.448, A.451, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.448, B:I.479, B:V.527, B:Y.530, B:Y.530 6OU.13: 18 residues within 4Å: Chain B: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Chain C: Y.584, L.585, L.588, S.629, L.630, Y.631, C.634, L.635, F.638 Ligands: 6OU.4, 6EU.19 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:I.660, B:I.661, B:L.664, C:Y.631, C:F.638 Salt bridges: B:K.656, B:K.656 Hydrogen bonds: C:S.629 6OU.15: 18 residues within 4Å: Chain A: Y.584, L.585, L.588, S.629, L.630, Y.631, C.634, L.635, F.638 Chain C: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6EU.3, 6OU.20 8 PLIP interactions: 5 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:I.660, C:I.661, C:L.664, A:Y.631, A:F.638 Salt bridges: C:K.656, C:K.656 Hydrogen bonds: A:S.629 6OU.18: 15 residues within 4Å: Chain C: F.448, A.451, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.448, C:I.479, C:V.527, C:Y.530, C:Y.530 6OU.20: 13 residues within 4Å: Chain A: L.585, V.586, F.589, T.593, L.630 Chain D: I.446, T.449, A.450, Y.453, Y.454, W.549 Ligands: 6OU.15, LBN.21 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:F.589, A:F.589, A:F.589, A:F.589, D:W.549, D:W.549 Hydrogen bonds: D:Y.454 6OU.22: 18 residues within 4Å: Chain B: Y.584, L.585, L.588, S.629, L.630, Y.631, C.634, L.635, F.638 Chain D: K.656, A.657, I.660, I.661, L.664, A.665, I.668 Ligands: 6OU.10, 6EU.12 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain D Hydrophobic interactions: B:Y.631, B:F.638, D:I.660, D:I.661, D:L.664 Hydrogen bonds: B:S.629 Salt bridges: D:K.656, D:K.656 6OU.24: 13 residues within 4Å: Chain B: I.446, T.449, A.450, Y.453, Y.454, W.549 Chain D: L.585, V.586, F.589, T.593, L.630 Ligands: 6OU.6, LBN.14 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: B:I.446, B:W.549, B:W.549, D:F.589, D:F.589, D:F.589, D:F.589 Hydrogen bonds: B:Y.454 6OU.25: 15 residues within 4Å: Chain D: F.448, A.451, A.452, V.475, E.478, I.479, S.481, V.482, M.523, S.526, V.527, Y.530, F.531, Y.537, M.541 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:F.448, D:I.479, D:V.527, D:Y.530, D:Y.530

4 x 6EU: resiniferatoxin(Non-covalent)

6EU.3: 27 residues within 4Å: Chain A: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.577 Chain C: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.15 17 PLIP interactions: 15 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:F.507, A:Y.511, A:L.515, A:L.515, A:F.543, A:L.553, A:A.566, A:I.573, C:L.669, C:L.669 Hydrogen bonds: A:Y.511, A:T.550, A:T.550, A:R.557, A:R.557, A:E.570 pi-Stacking: A:Y.511 6EU.12: 27 residues within 4Å: Chain B: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.577 Chain D: F.587, F.591, L.662, A.665, I.668, L.669 Ligands: 6OU.22 17 PLIP interactions: 15 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.507, B:Y.511, B:L.515, B:L.515, B:F.543, B:L.553, B:A.566, B:I.573, D:L.669, D:L.669 Hydrogen bonds: B:Y.511, B:T.550, B:T.550, B:R.557, B:R.557, B:E.570 pi-Stacking: B:Y.511 6EU.19: 27 residues within 4Å: Chain B: F.587, F.591, L.662, A.665, I.668, L.669 Chain C: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.577 Ligands: 6OU.13 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.507, C:Y.511, C:L.515, C:L.515, C:F.543, C:L.553, C:L.553, C:A.566, C:I.573, B:L.669, B:L.669 Hydrogen bonds: C:Y.511, C:T.550, C:T.550, C:R.557, C:R.557, C:E.570 pi-Stacking: C:Y.511 6EU.26: 27 residues within 4Å: Chain A: F.587, F.591, L.662, A.665, I.668, L.669 Chain D: F.507, Y.511, S.512, I.514, L.515, F.516, V.518, F.543, A.546, M.547, T.550, N.551, L.553, Y.554, R.557, A.566, I.569, E.570, I.573, L.577 Ligands: 6OU.6 17 PLIP interactions: 15 interactions with chain D, 2 interactions with chain A Hydrophobic interactions: D:F.507, D:Y.511, D:L.515, D:L.515, D:F.543, D:L.553, D:A.566, D:I.573, A:L.669, A:L.669 Hydrogen bonds: D:Y.511, D:T.550, D:T.550, D:R.557, D:R.557, D:E.570 pi-Stacking: D:Y.511

2 x NA: SODIUM ION(Non-functional Binders)

NA.7: 6 residues within 4Å: Chain A: G.643 Chain B: G.643, M.644 Chain C: G.643, M.644 Chain D: G.643 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.643 NA.8: 4 residues within 4Å: Chain A: Y.671 Chain B: Y.671 Chain C: Y.671 Chain D: Y.671 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Y.671

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kwon, D.H. et al., Vanilloid-dependent TRPV1 opening trajectory from cryoEM ensemble analysis. Nat Commun (2022)

Release Date

2022-06-01

Peptides

Transient receptor potential cation channel subfamily V member 1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Membrane

We predict this structure to be a membrane protein.
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Transient receptor potential cation channel subfamily V member 1

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